I found the solution. Mantis creates a config data set in the "mantis_config_table" while creating the data table.
If one deletes this data set (for a plugin "Test" it would be the set with config_id "plugin_Test_schema") or sets the value to -1 one is able to upgrade/create the data table if not available in the data base yet. You can do this as administrator in the "Manage / Manage Plugins" menu.
Hint: It is also possible to edit/delete the config directly for your plugin as administrator in the "Manage/ Manage Configuration" menu.